Doug Hadley, a spokesman for the Halifax Regional School Board, would not reveal whether the workers were fired or whether they quit. He would only say the two are no longer employed, effective Friday.
"We have gathered enough information to confirm that an incident took place that was inappropriate, demonstrated very poor judgment and caused potential harm to a group of students," Hadley said in a statement.
"We regret this incident has occurred and we apologize to the students and parents involved."
Parents at Bedford South School complained to officials and alleged 10 to 12 students involved in the Excel after-school program had their mouths taped shut by an assistant instructor. There are 90 kids in the program and seven staff members were working on May 16 when the incident occurred.
One mother told CBC News her seven-year-old son complained that his mouth had been taped shut and he was told that if he tried to take it off, it would be put back on.
Two employees were sent home on paid leave after the incident came to light earlier this week.
Hadley said the investigation by the Halifax Regional School Board is concluded, although a Halifax Regional Police investigation continues.
"Our number 1 concern rests with protecting the health and safety of our students. As an organization, we will be reflecting on our existing practices to determine if any changes are necessary to better support children in the before and after-school programs," he said.
"We have been asked by police to not publicly discuss details as there is an ongoing police investigation."